| cghCall {CGHbase} | R Documentation |
Container for aCGH data and experimental
metadata. cghCall class is derived from
eSet, and requires the following matrices of equal dimension
as assayData members:
copynumber Log2 copynumber ratios.
segmented Segmented log2 ratios.
calls Called copynumer values.
probloss Loss probabilities as returned by CGHcall.
probnorm Normal probabilities as returned by CGHcall.
probgain Gain probabilities as returned by CGHcall.
probamp Optional amplification probabilities as returned by CGHcall when run with nclass=4.
Furthermore, columns named Chromosome, Start, and End are
required as featureData members, containing feature position information.
Directly extends class eSet.
new('cghCall',
phenoData = [AnnotatedDataFrame],
experimentData = [MIAME],
annotation = [character],
copynumber = [matrix],
segmented = [matrix],
calls = [matrix],
probloss = [matrix],
probnorm = [matrix],
probgain = [matrix],
featureData = [AnnotatedDataFrame],
...)
An object of class cghCall is generally obtained as output
from CGHcall.
Inherited from eSet:
assayData:nrow(phenoData). assayData must contain the following matrices
copynumber Log2 copynumber ratios.
segmented Segmented log2 ratios.
calls Called copynumer values.
probloss Loss probabilities as returned by CGHcall.
probnorm Normal probabilities as returned by CGHcall.
probgain Gain probabilities as returned by CGHcall.
probamp Optional amplification probabilities as returned by CGHcall when run with nclass=4.
assayData. Class:AssayData-classphenoData:eSetfeatureData:AnnotatedDataFrame with columns
Chromosome, Start, and End containing array element position
data.experimentData:eSetannotation:eSetClass-specific methods.
copynumber(cghCall), copynumber(cghCall,matrix)<-copynumber in the AssayData-class
slot.segmented(cghCall), segmented(cghCall,matrix)<-segmented in the AssayData-class
slot.calls(cghCall), calls(cghCall,matrix)<-calls in the AssayData-class
slot.probloss(cghCall), probloss(cghCall,matrix)<-probloss in the AssayData-class
slot.probnorm(cghCall), probnorm(cghCall,matrix)<-probnorm in the AssayData-class
slot.probgain(cghCall), probgain(cghCall,matrix)<-probgain in the AssayData-class
slot.chromosomes, bpstart, bpendfeatureData
See eSet for derived methods.
Sjoerd Vosse
eSet-class, cghRaw-class, cghSeg-class
# create an instance of cghCall
new("cghCall")
# load an instance of cghCall
data(WiltingCalled)
# plot the first sample
plot.cghCall(WiltingCalled[,1])
# plot the first chromosome of the first sample
plot.cghCall(WiltingCalled[chromosomes(WiltingCalled)==1,1])
# get the copynumber values of the third and fourth sample
log2ratios <- copynumber(WiltingCalled[,3:4])
# get the names of the samples
sampleNames(WiltingCalled)
# get the names of the array elements
featureNames(WiltingCalled)